Hi All,
I am trying to perform the cuffmerge operation on a couple of samples after cufflnks. I am using the gencode.v12.annotation.gtf as the reference file. My command is as follows
cuffmerge -o CN_cuffmerge -g gencode.v12.annotation.gtf Assembly_GTF_list.txt
Cuffmerge fails with the following error
[Sun Oct 28 23:39:46 2012] Comparing against reference file gencode.v12.annotation.gtf
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
Error: duplicate GFF ID 'ENST00000361547.2' encountered!
[FAILED]
Error: could not execute cuffcompare
Curiously, when i run cuffcompare separately using the same gtf file and it works (from another thread on seqanswers it appears that this might be because of cuffmerge does a RABT).
Same issue was posted here http://seqanswers.com/forums/showthread.php?t=21364 by somebody else, but there were no replies to it. Hence trying one more time. Help greatly appreciated.
Regards,
ngs_newbie
I am trying to perform the cuffmerge operation on a couple of samples after cufflnks. I am using the gencode.v12.annotation.gtf as the reference file. My command is as follows
cuffmerge -o CN_cuffmerge -g gencode.v12.annotation.gtf Assembly_GTF_list.txt
Cuffmerge fails with the following error
[Sun Oct 28 23:39:46 2012] Comparing against reference file gencode.v12.annotation.gtf
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
Error: duplicate GFF ID 'ENST00000361547.2' encountered!
[FAILED]
Error: could not execute cuffcompare
Curiously, when i run cuffcompare separately using the same gtf file and it works (from another thread on seqanswers it appears that this might be because of cuffmerge does a RABT).
Same issue was posted here http://seqanswers.com/forums/showthread.php?t=21364 by somebody else, but there were no replies to it. Hence trying one more time. Help greatly appreciated.
Regards,
ngs_newbie
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